sanguinemare

August 24, 2017

Be curious, and listen to their stories

I think if there’s anything that I’ve learned so far in the wards, it’s that you really never know what someone has been through unless you ask.

Case in point: Today, I found out that one of my attendings not only used to be a competitive football player (which I’d found out a couple days ago when I first met him… before I knew he was an attending by the way…), but had also served (and still is serving) as a surgeon in the Air Force for 16 years in Special Operations.  If I remember correctly, apparently, the former makes him one of only about 80 surgeons serving about 350,000 soldiers in the Air Force, while the latter category puts him in a group of even fewer surgeons, who actually travel with the soldiers and do emergency surgeries wherever they are in the field (as opposed to serving in a military base).  He also did his residency at a military hospital where there were no surgical specialty residents, which meant that there were no ENT, orthopedics, neurosurgery, etc residents, so they had to basically learn how to do every single type of surgery, which is awesome (I really really wish we had more of those programs!).  He has been deployed multiple times overseas, and he shared some of what it was like to work in those conditions.  What they had to work with was whatever they could carry on their backs, and he showed me some pictures of what he did in the field with the limited equipment they had (including craniotomies, which is basically cutting open the skull to release pressure!).  We also talked about how there (and even now sometimes), if someone’s about to die, sterilization is not of concern.  They just go at it with whatever they have in the quickest way possible, and sometimes even use things in succession from one patient to the next in times of crises.  It’s kind of shocking to hear/think about now, in our world of antiseptic cleanliness, to not even use a flame to sterilize instruments before use.  But it totally makes sense too, in that context.  “Sure, they might get an infection later, but we’re saving life and limbs out there!  They might get an infection, but at least they’re alive.”  Good point.

In my mind, the term “doctor” has always evoked two images – that of a family/local physician, who treats everyone and everything, and thus essentially is the best primary care/internist there is… or that of a surgeon on the battlefield, with the wounded all around, desperately fighting to save lives.  The latter is what he has lived through, which is amazing.  And he loves it.  I did have to ask, as this is something I have often wondered/felt it would keep haunting me if I attempted to go that route – “How do you deal with having people die in your hands?  Do you ever worry that something you did caused the death of the patient, or caused them even more misery before they die anyway?”  His answer was practical in its simplicity: “Well, if they die, they were going to die anyway.  Or they’ve already died, and we’re trying to resuscitate them.  You can’t do anything worse to them than what is already happening, which is death.”  Well, guess I can’t really argue against that one.

All of this I never would have known if I’d just assumed he was like any other resident/attending when I met him.  Granted, he’s a pretty big/strong guy, and has multiple tattoos, which I guess isn’t the most stereotypical picture of a surgeon, but still.

There are many other cases like that too, but with patients.  While I was at the VA last month for the 2nd half of my IM rotation, I learned about one man’s time in the Navy, where he spent 10 years at sea and lost two wives in the process (he was supposed to spend 4 years at sea and 4 on shore, but he got the short end of the stick and somehow was never given shore duty), and also got cancer, which they think may be secondary to his being on Christmas Island during the atomic bomb testing.  He said they’d been ordered to literally run under the cloud that formed after detonation for as long as they could, which is a pretty crazy breach of human ethics I would think.  But anyway, he also humorously recounted his first trip to Fiji, where 19 year old him was pretty shocked at the sight of the women at the time, who had rushed up to the boats in their native dress, which was topless.

Another veteran told me about how he was fully deaf in one ear and only had 30% hearing left in his other because they blew a cannon right over his head, and that his team of ~32 was able to rescue a whole platoon of about 85 people out alive during the Korean war without losing a single person… but when he got back, the US government lost his record, so he never got any recognition for it.  His story was pretty crazy too – he then ended up smoking and drinking for 42 years, “drunk for the last 14 years”, due to depression from all that happened during his 8 years of service in Korea. Then he had a seizure due to drinking too much on the day before he planned to suicide (by dynamite in a mine shaft, no less) but he says God found him, and he quit both cold turkey and hasn’t been tempted to try again since.  Amazing.  He was also the one who told me “I’m glad it’s you” when I was about to leave after taking his H&P (history and physical exam), and when I stopped and looked at him questioningly, he elaborated with “you’re very thorough, and you seem to really know what you’re doing.”  While I certainly don’t think was an accurate statement for me haha, it was still a very nice sentiment, which I thanked him for.  I ended up having the day off the next day, which is when he got discharged, so I never did get to see him again after rounds or to say bye.  But I hope he healed up and that he continues to do well.

There was another vet, who everyone kept saying was “just crazy/psychotic” because he would talk a lot and seemed fixated on certain ideas.  I went to talk with him, and it does seem like he has anxiety and probably OCD, but I also learned that his PTSD came because he had served in Russia back in the day, when they were on a secret mission I think.  He had been riding around the perimeter with the captain to hear the scout reports, and were on the way back when they found the troops burning in their tents.  He and the Captain rushed in and attempted to save them, but they couldn’t save a single one.  He still remembers it vividly, and feels great guilt over it, but it seems like he hasn’t really told anyone else about it.  I suggested that he find someone to talk to about his experiences to help him through that and his anger issues with his mother, who he clearly loves very much, but gets frustrated by because she no longer treats him like her trusted, beloved son after he blacked out from drinking too much 13 years ago (likely due to his unresolved PTSD and other issues) and never listens to him anymore.  He says he cries after he yells at her and she leaves, and was almost in tears while telling me, but he says he can’t help getting frustrated when they talk regardless.

So many people I think really just need people in their lives to just listen.  No degree is even necessary for that.  Just listening to someone and not judging them can help so much I feel.  But unfortunately in this world, so few people truly have time for that.  Which, I guess, is one of the few blessings, and privileges, we can give/get to our patients as medical students.  The gift of time, as well as an ear to hear, and perhaps even a shoulder to lean/cry on.  Which brings me to my last example – a patient who wasn’t even mine to take care of, but was on our team’s service.

This was a man almost my own age who had been brought in for an overdose on cocaine and probably methamphetamine.  He had been found on the street, yelling at a policeman, and was brought in.  He had multiple lacerations on his arms, and when he had first come in the previous afternoon, the upper level resident I was working with had said “don’t bother” seeing him, I think perhaps because she felt it was a simple case to manage medically and I wouldn’t really learn anything.  However, on rounds the next morning, after some questioning by our attending (during which I found out he’d also apparently re-activated his Hep C), he muttered a few things that I found troubling – that it happened because he “was around people he shouldn’t be around,” that he didn’t want to get treated for Hep C because he had no money since his fiduciary wasn’t giving him his payments so “it’s ok, I’ll just clear it on my own, like last time,” he knew he “shouldn’t be doing this, because every time it happens, I just end up shooting up and having a lot of sex…” and when we then questioned him then how he got the money for the drugs, he said something that sounded like “well, I kinda just you know, sell myself I guess.”  The picture I was getting from this hurt my heart, and so when I found out he was going to get transferred that afternoon to a different service, I made it a point to visit him to try to get to know him a bit more before I had to go to class, hoping I could maybe help him somehow.  At first, he was very reluctant to talk, but when I mentioned his potential transfer and how I might not see him again, I think he realized I cared and at least stopped acting like he wanted me to go away.  I didn’t get all that more out of him, but I did find out that he served in Iraq, and I think he had a very hard time and hasn’t been able to talk to anyone about it.  When asked why he did the drugs, he said “I just don’t want to be me.”  When asked what he meant by that, he just shrugged defeatedly and responded “I don’t know. I just.. hate myself. I don’t want to be me. That’s all.”  I also asked why he was moving states to begin with, as I’d noticed that in his notes, and he said “I was trying to get away from people I shouldn’t be around.  But I’m starting to realize it doesn’t matter, because you can find them anywhere.”  I also tried to advise him to find someone to speak to about all of this, even if it was hard at first, because everything he’s going through is not something that someone can carry alone, and his current trajectory was not good, and he knew it too.

Through this, it was so painfully clear that he wasn’t a drug addict and engaging in these behaviors for the fun of it or even maybe for the physiological high.  He obviously wanted to stop but didn’t know how… because the whole reason he fell into it in the first place was because he was depressed and trying to numb his pain (in fact, his file has a “suicide risk” warning flag that pops up when you open it), and he couldn’t see any way out of his darkness.  I could say a lot here about my now much stronger feelings regarding drug dealers who prey on this type of person, but that’s a rant for another time.  Overall, I just thought his whole story was heartbreaking, and I actually ended up almost breaking down in that room after I said some encouraging words to him that I could tell almost made him cry, and then when I got upstairs to our team room (which was thankfully empty), I just let it all out.  Here was a life that still had so much potential, and yet he was stuck in this dark place all alone, and even we, who are supposed to be health providers, are not able to do what needs to be done to help him, because of the way the system is set up.  He was just going to get discharged after he cleared the drugs, but if there’s no one to talk with him and follow up with him, he’s just going to end up the same way and end up back in the hospital and the cycle will continue, or worse, one day he might overdose and die.  I sincerely hope that is not the case, and that hopefully my words, or someone’s words, will have a good impact and change his life around – perhaps that he will find God as well, like the second vet I mentioned, and be able to see that his life does have worth, meaning, and life.  But regardless, my heart breaks for him and where he is right now, and for everyone who is in a similar situation.  And for all of our vets, who go through so much for our sake’s.

The sense I get from healthcare providers about the VA is often frustration with the system, jadedness about both caregivers and patients, and a kind of resignation, that the patients are all “a certain type.”  And yes, that’s generally true – there is a lot of substance use/abuse in this population, which leads to many of them having heart, lung, and/or kidney issues, and many of course have PTSD or other psychological issues (and amputations).  But really, who can blame them, given what they’ve been through and how (some of them) have been treated when they come back?  It’s a very isolating experience, and for the most part, we as a society are not well-trained in helping people through that.   So don’t be that healthcare person who just writes off a patient because of their addiction or psych issues.  Be the one who listens – the one who learns about the hidden stories.  Everyone has struggles and life experiences that you would never know if you just judge who they seem to be today.  Be curious.  Ask questions.  Spend time.  And just listen, with an open, non-judgmental, and loving heart.  You just might learn something – and in return, you just might end up giving a greater gift of healing to these people than any of the medicines and procedures we’re taught about can reach.

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In completely unrelated news, I also found out my Shelf exam score today for my last rotation and… I passed!  I didn’t get high enough to get honors, but honestly, that test was so unexpected and random in the questions asked (very few on cardio, pulm, and renal, and a lot more than expected on trauma, skin, heme/immunology/inflammation and other random facts) that it was the first test I walked out of actually concerned I might have failed, so I’m thankful that I made it :).

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August 3, 2017

Ear irrigation and Dix-Hallpike Maneuver and Updates

Today was an interesting day!  Surprisingly mostly because of clinic rather than what’s been going on in the in-patient setting.   So much a bit of background – I’ve switched over to the VA for the month on a different team, and we go to clinic once a week as well to experience what things are like at the outpatient setting.  The first time last week was a little hectic – my preceptor had just come back from a week of vacation and had a lot of catching up to do, so it was a bit of a whirlwind.

Today at clinic though, I actually felt like I was able to participate in the healthcare a bit, which was nice – I am starting to realize I would like to be able to do procedures/work with my hands at least a little with the patients.  Currently in the in-patient setting, I feel like my role has mostly just been talking to people (either patients, other team members, or making phone calls) and looking things up on the internet, but it’s mostly theoretical/medical management, and not as much hands-on.  But today during a routine check-up at the clinic, I got to help out with an ear irrigation due to earwax plugging up of ears leading to decreased hearing (and the patient was actually more comfortable when I did it I think), which was something I’d always heard about but never saw in real life.  Basically, she added drops into one ear (5-10) to soften the wax, then plugged it up with cotton and turned the head over to repeat on the other side.  Then they prepared a spray bottle with lukewarm water, attaching a small, flexible tubing to the end, and then removed the cotton, put the tubing into the ear, and gently spray into the ear until the earwax/dissolved debris runs out (don’t forget to put towels below and use a container to catch the water!).  Also don’t spray too hard, or it’ll 1) be painful for the patient and 2) it’ll spray all over you when it comes back out!

I also finally got to see how to do the Dix-Hallpike maneuver in person!  The latter was pretty exciting to me (even though the move actually turned out to be quite simple) because I’d had a patient with unexplained vertigo last month at the hospital that I thought might have BPPV, but since I didn’t know how to do it and no one on my team had done it before either, I wasn’t sure if I should try it, especially since she was so dizzy at baseline.  But now I know!  Essentially the person sits on the bed, turns their torso to a 45 degree angle, and they are supported down to the bed straight down in that manner (without turning their torso back to a supine position), to see whether they get dizzy.  As an aside, I did end up trying the Epley maneuver on that previous patient to try to improve her symptoms, but it was hard to tell which side was worse for her, and I don’t think it did anything much but make her more dizzy… :\  The one thing that did seem to help though, was talking to her and listening to her – she’d had a lot of really sad things happen to her children/family over the last few months, including deaths, stroke, diagnoses of cancer etc, and so talking with her and praying with her on the last day of her stay I think did much better than anything else we’d done for her during her stay.  I’m grateful I had that opportunity.  May God watch over and comfort that family.

June 30, 2017

Week 1 of clerkships, and a little bit about the dissertation submission process

Today marks the end of my 1st week back to medical school, as a 3rd year student on the wards.  (Is it more grammatically correct to say “in the wards” or “on the wards”?  Hmm…) It’s been a pretty crazy ride so far, and I have to say, post-call day was pretty brutal.

So just to walk you through my week, I’ve basically been waking up around 6am this week to make it in on time at 7am (and I’m fortunate that my commute is about a <10 min walk) to be able to look up what happened to my patient overnight, check in with them, and get my thoughts organized before we round at 9am.  Generally I’ve been staying until around 4:30-5pm, sometimes just to go over my notes for the day.  On call day (Wednesday this week – it happens every 5 days), I got in at around the same time, but stayed until ~9pm, and post-call day, I had to wake up at ~4am to get in at 5am to prep for rounding at 7am to go over the patients the night shift team needed to pass over to us.  I still got out around 4:30pm that day.  So as you can imagine, that’s been pretty rough.

After I get back, I’ve been working on revising and sending out our manuscript the first couple nights to a new journal, and then yesterday I got an e-mail about minor edits for my dissertation, so I spent a couple hours fixing that on post-call night (after first taking a nap for a couple of hours), and finally got the final acceptance for that this morning.  Whoo hoo!  That also means I haven’t had any time to study/catch-up yet though, so I’ve been doing pretty poorly in terms of answering questions from the attending/residents.  It’s to the point where our attending didn’t even bother asking me questions when he went over antibiotics with us this afternoon, which is pretty much when you know you’re in bad shape. Sigh.

Anyway, also just wanted to give a brief overview of the dissertation submission process, (at least at our school) since I haven’t had a chance to yet, and did just happen to finish that today.  Basically, ~2 weeks before the PhD defense, you’re supposed to submit your dissertation to all of your committee members.  They review the file, and depending on the department, they’ll either give you feedback before your defense, or after.  My department does that after for some reason, so I didn’t see any edits until after my defense.  Then, you have 10 business days (aka 2 weeks) to make all the edits your committee requires, which can be either minor or extensive, depending.  Mine were pretty minor for the most part, luckily, but since I’m somewhat of a perfectionist, I also went back and fixed wording, added citations, fixed figures, etc.  That last one took an extremely long time to figure out because Microsoft Word for some reason was not converting pictures right, so I tried asking for help, and that person didn’t get back to me until the day before it was due (and actually they made one thing worse and didn’t fix any of the issues at all), so it was quite a bit of a panic there at the end.  Extremely fortunately for me, I was supposed to meet up with a computer engineer friend for lunch that last day, and he finally figured out the rather crude, but effective, method of print-screening the figures really large on a big monitor and copy-pasting into Word.  So there’s a tip for you, if you ever have issues with importing images into Word!

Anyway, after finally submitting it, then we wait until the graduate school looks over it and sends an e-mail with any formatting or other issues that need to be fixed.  I got that e-mail yesterday, made my revisions (and went through everything again with a fine-toothed comb to check for (many) spacing errors and typos), sent it in, and got the e-mail back this morning saying it was officially accepted.  Apparently sometimes that last step can go back and forth for a bit – another MSTP who went back a rotation before me and is now on the same rotation as me said it took him a couple weeks of going back and forth with the graduate school before it got accepted, but I think he also didn’t realize that some of his changes threw off other formatting, so maybe that’s why it took longer.  But anyway, there you have it!  That’s the dissertation submission process in a nutshell.   And it’s past my bedtime nowadays, so goodnight!

June 26, 2017

First Day Back to Clinics

Filed under: Med School and the MSTP,MS-3 — sanguinemare @ 7:07 pm
Tags: , , , ,

Thoughts and impressions about my first day starting back as an MS-3 student on the wards (on Internal Medicine):

Orientation:

Orientation was pretty chill, but unfortunately less informative than I would have liked, in regards to say… what my actual schedule was going to be like (which, if nothing else, I was hoping we’d at least get some sort of understandable schedule.  Someone even had to ask what call/post-call meant, because there was no explanation of the hours or caps or anything in the actual orientation.  FYI, I’m still not actually sure what it entails, but from what my MSTP friend told me yesterday at retreat and somewhat from orientation today, I gather that there’s something called a “short call”, which goes from ~7am-12pm, with a cap of 4 new patients.  “Long call”, means 12pm – 8pm or so (which is when night shift gets there), with a cap of 8 new patients (and takes over if the short call team caps).  Except here’s where I get a little confused, since my interns mentioned that on our call day, we also start rounding at 7am, which also means we need to get there around 5am.  So, not really sure on that… and then “post-call” is apparently the day after long call, where we also have to be in to present by 7am.  So basically post-call days are probably going to be the worst in terms of sleep deprivation and such (but even then, as med students, we don’t have it nearly as bad as the interns).

The other 3rd years on this rotation seem pretty chill though, which is nice.  Also got to see an old acquaintance who used to be a year above me, went to Harvard for his PhD, then came back to 3rd year here, so that was nostalgic.  Apparently he’s been back since January.

The team:

We have a pretty full team – 1 PGY-3 (3rd year resident), 2 PGY-1’s (interns), 1 4th year, and 2 3rd years.  It’s good I guess so the work is split more, but it also means so that we are down 1 computer in our team room, which worked out ok today because I still didn’t have computer access yet, but will be kind of a problem later.  I ended up having to grab a “COW” (computer on wheels) after I was finally able to get access to the online system this afternoon, and that was a bit tricky to use because it was kind of cumbersome/blocked a large part of the room, happened to have a broken lever so wasn’t height-adjustable, and just wasn’t great to have to use overall.  Actually now that I think about it, I’m probably going to have to use another one tomorrow, since it sounds like everyone else is planning to get there super early, and I’m only planning to get in around 7am (one of the interns said we just needed to be ready by 8am, but it sounds like the 4th year wants to be in IM so is going to get there really early, and the other 3rd year also seems like he’s going to wake up early), so the computers will likely be all taken up by the time I get there. Ah well.

In terms of the people, our group seems pretty nice and friendly.  It’s apparently almost everyone’s first time though, which makes for an interesting dynamic.  This is the interns’ first rotation, the first AI for the 4th year, obviously the first rotation for me, and the upper level resident’s first time on this service.  The only one whose first time it isn’t is my co-3rd year, and it’s only his 2nd rotation.  So far though, other than the interns and 4th year all looking extremely tired (which is actually rather concerning…) everyone seems pretty friendly.  It’s also kind of interesting because our upper level is actually someone from my class haha.  So that was fun.  (And thankfully he’s super nice and really wants to teach people, so I’m glad it was him).  Our attending seems pretty laid back as well, but we’ll see.  He actually invited us to his place for a party on Saturday this morning haha!

My mental status after today:

Wow.  I am so lost, and know absolutely nothing.  We saw a patient with bullae and the only thing I could think of was “epidermolysis bullosa,” but when the attending asked us the most likely cause, I had no idea.  The other med student didn’t skip a beat, and said “antibodies”, and I had no idea what he even meant.  (And now that I’ve looked up EB, which is apparently usually genetically based, I’m pretty sure that wasn’t even correct…)  And what with all my access being limited and everything else, I was essentially completely useless on the team today.  I have a LOT to learn.  Which is why I need to buy the UWorld Qbank tonight and start doing some questions right away haha.  It’s going to be tough to get back up to speed in such a short time, but I’m going to do my best.  I also need to submit our manuscript which got rejected over the weekend to another journal, and still need to re-draft another manuscript and edit some other files, as well as read up on my patient tonight.  Yikes.  Now I know why everyone says 3rd year is really tough (aside from intern year).  There’s really no time to waste on any unnecessary things.  Well, I guess it just means it’s time for me to finally learn to be efficient with my time!  Wish me luck!

April 27, 2017

Got the green light to write! (And a little about the graduation process)

Filed under: "Me" updates,Grad school,Research — sanguinemare @ 1:08 am
Tags: , , ,

Today, I had my (hopefully) last committee meeting before my thesis defense.  Basically, I presented the data I had thus far and asked whether they thought I had done enough work to graduate in the summer.  They said yes, praise God!  So I will be defending my thesis in early June, in time for starting medical school on schedule at the end of June (well, actually I found out that the rest of the class actually starts next week, oddly enough, on block “6A”, whereas the end of June one is called “1A”, but anyway…). The timing only gives me a week or two at home before starting back again, but at least there’s a little break, and it gives me an extra two weeks or so to write than I would have had if we’d done it at the end of May (my PI is out of town until early June, so that was the earliest that was feasible).

I’m not sure if it’s the same at all schools, just to walk you through the graduation process a bit, here’s our rough graduation process.  After the committee agrees you can graduate soon, we have to turn in an “application for degree form”, after which the graduate school will give us an approval form that we need to fill out and return to them 2 weeks before our defense at the latest.  This form will be the official confirmation to the school that we are defending, and they apparently put it on a school-wide calendar.  We also have to turn in our entire written dissertation (usually ~100 pages long) to our committee 2 weeks before the defense date so they can read over all the materials in preparation for the defense.  Then, we have our public, oral defense, where we present our work over the last few years to the public, and then we have a private defense after, where the committee decides whether the student has enough proficiency in their area to be awarded a PhD.  If this thesis defense is passed, we then make the final edits to the dissertation and need to submit the written thesis to the graduate school, where I think it gets bound and also put online.

In my program, the thesis itself can be either in the traditional format (an introduction, a body which has multiple chapters describing work done, and a conclusion), or a “3-paper model”, where essentially 3 individual papers are written up, which become chapters in the dissertation, and they are sandwiched between an introduction and conclusion.  That’s the route I’m going, because it seems the simplest way, especially since I’ve gotten one paper published already.

Ok, time to head to bed – tomorrow’s the all-day orientation for MS-3 year (pretty crazy to think that it’s finally happening!) so better get some rest before that.

Until next time!

April 14, 2017

IT GOT ACCEPTEDDD~!

Filed under: "Me" updates,Grad school,Research — sanguinemare @ 1:16 am
Tags: , , , ,

Ok, a very unprofessional title, and about 10 days or so late (now that it’s officially the 14th, at least here), but just wanted to post a quick update that… after staying up until 4am a couple nights re-creating the figures from scratch because for some reason they were apparently not in good enough resolution the first time and the (semi-)quick fix didn’t work… MY FIRST, FIRST-AUTHOR PAPER GOT ACCEPTED (for publication)!!! WHOO HOO, PRAISE THE LORD!  That means I’m all set for non-thesis related graduation requirements!

Oh how easy it is to bring a grad student joy, haha.

Now all I have to do is… revise paper 2, do all the assays and writing for paper 3, and write an introduction and conclusion… all within a little less than a month now, plus a committee meeting in the middle of that.  Whew.  I’ve actually been pulling 13-14 hour days in the lab every day from last Tuesday until Sunday (minus Wednesday for weather concerns), and then averaging around 9 hours every day since. Apparently this is pretty typical during the end-stage – I ran into a fellow MSTP a year below me in the elevator the other day and after relaying my current schedule, and he was like “what are you doing, trying to graduate?” I blinked a couple times at the irony, then replied with a “why yes, actually!” with a bit of a cheeky grin, and he nodded understandingly, saying “ah, the extremely productive final year huh?”  On a bit of reflection, I suppose that is actually sort of true.  Everyone always talked about the last year being the most productive in terms of both experimental data gathering, and paper-writing, and I suppose technically that has somewhat been the case for me as well.  So there you go – “n of 1” as they say, haha!

Just finished organizing all the miscellaneous parts/templates for my thesis tonight.  It’s starting to feel a lot more real now.  Yikes.

Wish me luck!

March 29, 2017

Struggles of a grad student – Part 1

Filed under: "Me" updates,Grad school,Research — sanguinemare @ 1:49 pm

Today was the epitome of Murphy’s law for a grad student – the classic case of needing to order supplies for a key experiment, and the lab not having it… and then not being able to order it due to a series of unfortunate events: the supply center which I’d sent the order in to yesterday is apparently closing and not accepting any more orders –> the other person we place orders from has an auto-reply e-mail saying they are out having surgery and not to place orders until they’re back tomorrow unless it’s an emergency, then contact person b –> person b also has an automated e-mail reply saying they are out of the office today and won’t be responding e-mails until tomorrow –> another supply center that I found out about from the one that’s closing ALSO has an auto-reply e-mail saying they are out of town right now and will only intermittently check e-mail.  *Sigh*  At least that means I should be able to place an order first thing tomorrow, but it also means that’s another day’s delay before I can start the assays.  At least there’s a few other steps (aka days’ worth of work) that I have the resources for beforehand.

Generally this sort of thing can be avoided if 1) there is good communication in the lab (and/or a good lab manager and/or a good system in place so you can easily check the lab inventory), and 2) you plan ahead.  Both are good practices to have so you don’t need to delay your work just to wait on things to arrive.

Sometimes, however, it is not really avoidable, such as in this case, where the study only recently finished, I only just figured out how many samples I had total, and then found out that there’s a 384-well plate machine on the 2nd floor that we are allowed to use that would make my life a LOT simpler (less reagents used per sample and a lot less plates to run: 12 vs. 46)… but the catch is that we’d have to buy the plates ourselves.  So I decided to try to go for that, and that’s how this happened.  Also decided to order some different primers to try based on the literature, and those need to be custom-made and take time, so yeah.  Timing is so tight right now because I have a committee meeting set for the end of April, and the extractions and processing itself will likely take 2-3 weeks of full day schedules, plus analysis time and putting together a presentation (while writing 2 papers and my thesis).  Additionally, I just found out from the lab I was supposed to get my samples from today that because they aren’t getting in the new freezer until tomorrow, I won’t be able to access my samples until Friday afternoon after they’ve re-put everything back where it needs to be.  These are the little day-to-day things that people don’t really think of being part of research, but are snags that will affect how quickly things can be done.

Anyway!  At least the couple days’ reprieve from retrieving and processing samples means I have time to look over the short students’ Letter to the Editor I wrote with a couple students on a side project that just got accepted with minor revisions, as well as to re-draft my 2nd paper, which my PI and I just decided we should expand to a full manuscript yesterday (as vs. the Brief Report we were originally thinking of submitting it as – there are different lengths and purposes of publications, which I might get into in a future post if anyone’s interested).  So yeah, that’s life at the moment!  No rest for the grad student – at least not one who’s trying to graduate in a couple months.

Catch you guys later!

March 24, 2017

Just sent in my revision for my first paper! (And why that is a big deal)

Filed under: "Me" updates,Grad school,Research — sanguinemare @ 4:12 pm

HELLO all you lovely people (aka the 1 person who may actually see that I have finally posted after months of hiatus)!  I’m so sorry for dropping off the face of the planet, but well, PhD life is somewhat of a struggle and between that and battling long bouts of depression, it’s been difficult to drag myself up to write something substantial like this.  (I have also come to realize that I think almost all graduate students go through a mini existential crisis/period of depression before it’s over, unless they are extremely lucky and really love their work, mentor, and are extremely fortunate in their ability to generate and analyze data, but that is a story for a different day… if I ever get around to it, haha).

… and now that I actually revisited my last post, I realize I have somewhat reiterated myself, so I guess not much has changed over the last… 7 months?  Haha whoops.  Oh well.  Also apologies in advance for the somewhat incoherence of thought on this post as my brain is currently rather fried.

Anyway!

So I literally just clicked “submit” on my revision for my first paper.  This is a big deal for multiple reasons:

  1. It’s a graduation requirement. Of course, this is my first priority right now, so it gets to be first on this list 😛  As a graduate student, at least in the biomedical sciences, we are usually required to have at least one paper published under our name before we are allowed to graduate.  This is because, as I’ve mentioned in my last post, publications are essentially the “currency” of academia, and programs want to help their students show that they are competent and competitive in the scientific world, which will help with their upcoming job search.  The slightly less altruistic reason is that it also reflects well on the department/program/school/institution if they can show that a significant portion of their graduate student population are publishing good papers in peer-reviewed journals (important statistics for funding purposes).

    The publication requirements will vary based on said department/program, school (i.e. school of health professions vs. school of bioengineering) and institution, but my particular one requires at least 2 papers published before graduation, with at least one being a first author paper (*note: review papers – which are essentially summaries of a particular topic based on research that has already been published – do not count towards this second stipulation).  The paper that I have just turned in is my first, first-author paper, and thus is super important to get accepted since I am trying to graduate in May/June, and it has so far seemed to take an average of 2 months for responses from journals, which means timing is really tight right now. Speaking of which…

  2. Revision = higher chance of acceptance (?). Considering this is my first experience with submitting a manuscript, I’m not entirely sure how accurate this statement is, but from what I gather, a revision decision is usually a positive sign for a manuscript to get accepted into a journal for publication, especially if the revisions are minor.

    To give a little walk-through of this whole process thus far, I first started the analysis for writing up this paper a little over a year ago, ~Feb 2016.  The first complete draft was written by June, and after many (many) revisions, we finally submitted this article to a journal in August.  We waited for a long two months, during which one of my co-authors casually mentioned that perhaps it was actually a good sign we hadn’t heard in so long because she had also submitted to the same journal a couple weeks later and had already gotten a rejection letter.  She was right in a way, because in October, we got our paper back with reviewer notes, which is better than an outright rejection since it means that the editors thought it was at least interesting enough to send out to reviewers.  However, the journal ultimately rejected it after the review, though they did give us an option to do an internal transfer to another of the journals in their group.  We took that option and I did revisions based off of the reviewers’ comments.  We then resubmitted it to the new journal this January (there was a brief hiatus on this work as I was out of the town/the country for a little over a month between Nov-Dec).  After waiting another 2 harrowing months, we finally got the decision letter last week, which basically said they thought it was interesting, but reviewers had concerns which made it unacceptable at the present moment. Hopefully that means it will be acceptable after the changes…?  So I made the changes, and sent it in today. (Though a slightly concerning note at the bottom of the letter said that any decision after the revision was final, which induced a minor paranoia as I went to click the submit button earlier today. Heh).  Here’s to hoping it gets accepted!  Which brings us to the last point…

  3. (If accepted =) it’s a milestone as a scientist/researcher.  I kind of alluded to this above, but basically, having a first-author paper in a peer-reviewed journal helps to establish your worth to the scientific community.  The first author is the one who has generally been involved in all the aspects of the study, including conception/design of the study, conduction of the experiments, analysis, reading of the background literature, and writing the manuscript. Thus, in a way, a first first-author paper establishes the level of work others can expect from the author in the future, and is thus like a debut of sorts into the scientific world.

So yeah. In a nutshell, that’s why I’m actually quite happy with myself/life for once, and will likely take this weekend to celebrate (some of us in MSTP are going to Six Flags for a day!) before the massive freak-out session starting next week about how I only

Thanks for reading and see you on the other side (after my defense)!

August 31, 2016

Publishing and Reviews

Oh man, I can’t believe it’s been almost an entire YEAR since I last published here!  I’m so sorry… there’s been a lot going on, and also I’m fairly certain I’ve been actually depressed for the last year or so and only very recently started perking up a bit (like literally a couple weeks ago) so that’s probably part of the reason… PhD life and its ups and (mostly, at least in my case) downs, an unexpected and lengthy authorship battle… etc etc… so it was hard to find anything positive to write about, and/or to summon enough energy/brainpower to write about anything at length in general.  But that’s fodder for another post.

Today what I’m going to write about (briefly) is publishing!  Yay, publishing… the currency and lifeblood of the academic.  In case you weren’t aware, basically what, where, and how much you publish is an important factor for your career, mainly because all the people/agencies with money (institutions looking to hire you, government/other organizations looking to award grants) use it as a kind of surrogate measure of your scientific worth when evaluating whether or not to hire you/give you money.  In a way, it’s like judging you based on your contribution to society’s advancement, which I guess is fair, especially if you’re using, say, government funds to help your research. Where it gets a little tricky however, is when you get into the question of where the articles are being published, and whether quantity > quality, and that’s different for everyone.  There’s a whole discussion to be had about the Impact Factor of journals (which itself has some controversy based on how it is determined), but that might have to wait for another time.  In terms of quantity vs quality, from what I gather, I think (a very big emphasis on “think”) the general consensus is that quality is of course important, but publishing regularly (at least every year or so, even if it’s only a review paper) is highly desired because it shows consistency. Which is bad news for someone like me, who hasn’t even had a single (first author) publication yet, and it’s already my 4th/last year in the program (hopefully anyway), heh.

At any rate, after you submit your paper for publication, assuming it isn’t rejected outright, it goes to a couple reviewers.  These are usually other scientists, usually in a related field of study, but sometimes not.  They review the paper and help the editors of the journals determine whether the paper is ready to be either 1) accepted as is, 2) accepted with revisions, or 3) rejected.  The first two options are obviously preferred 😛 but if it needs to be revised, the manuscript authors need to address all the reviews (either by doing more experiments or rebutting with explanations why they don’t need to), and resubmit.  This process I hear can take anywhere up to a few weeks to a few months!  I just submitted my first PhD-related paper a couple weeks ago, so will try to update on how that process goes after I hear back.  It is currently in the “under review” status (so at least that means it wasn’t rejected outright, hopefully!)

Anyway, what actually prompted this post was that I got an e-mail from the director of the pre-doctoral training fellowship I’m currently on as a follow-up to a discussion we had about hosting a seminar for all the trainees to learn how to review a paper (something we will all be called to do as scientists in the future).  It was quite an amusing article on how to review papers by Greg Gibson, who apparently was a section editor for PLoS Genetics for 10 years, which exemplifies the type of feedback that was often receive from these things… and really, now that I think about it, it must be pretty difficult to have to constantly make executive decisions as an editor as to whose review gets the most weight if they are this scattered, haha!  But anyway, just wanted to re-post that all here for you guys in case you’re curious how these things work.

Until next time!  (Which will hopefully be less than a year from now! ^.^||)

October 8, 2015

Antibacterial Soap is not Better than Regular Soap… and learning from death

So, fun fact of the day: according to our MSTP seminar speaker tonight, apparently the FDA agrees that “antibacterial” soap is not any more effective at preventing disease transmission than regular soap, assuming both are used to wash hands properly!  Did not know that.  And to back that up, here’s an article straight off the FDA site that speaks about that, from 2013.

He also described a painful experience he had had as a clinician, where he did a procedure on a patient, and that patient ended up dying, even though he had done everything technically right.  This, in itself, was one of his lessons – that you can be technically right, but mess up intellectually.  Because, as it turns out, after that, they did a retrospective study, and apparently that patient was at high risk for bleeding out after that procedure, as they’d had a bone marrow transplant before that.  That wasn’t known at the time, but it cost that patient their life.  There are two lessons I learned from this:

The first, which is rather scary and sobering, is that as a doctor, we’re all going to make mistakes at some point.  Mistakes that may even cost people their lives.  And some of them, like the case here, won’t really be our “fault”, in the sense that it wasn’t anything that could be prevented at the time due to lack of knowledge, but in hindsight, for whatever reason – new research coming out, a new technique our clinic/hospital was not aware of, etc… we’ll realize that our decision at that point in time was what directly or indirectly, caused harm to the patient.  To be quite honest, that scares me quite a lot.  I don’t know if I can handle that. I think that would tear me apart from the inside.  And yet… if no one makes those decisions… even more people may come to harm.  It’s a tough job.  I guess time will tell.  I just pray that over the course of my career, I will be fortunate enough not to do anything so bad that it costs a life or cripples someone the rest of their time on earth.

The 2nd is that even in one’s darkest moments/worst mistakes, something good can come of it.  In this case, research that probably has saved at least a few lives since.  He recognized that maybe there was something about this patient that made them susceptible to the procedure, even though he did nothing wrong, and they went back and looked at records and realized this predisposition, and published a paper on it.  So now, anyone encountering this type of patient before this procedure will know that it is a high risk thing to do in these people, so they may be much more cautious about ordering that test to be done.  So even when making mistakes, analyzing it and building off of it may lead to research that helps others in the future.  And I guess that’s how we have to look at it, in order to keep moving forward, lest we crumble from the guilt and sadness of those we were unable to help.

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